# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 01:32:58 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 5-[(3R)-3-(5-methoxy-3',5'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(c1)c2cc(C)cc(C)c2)[C@@H](C)C#Cc3c(C)nc(N)nc3N
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 53T  53T  5-[(3R)-3-(5-methoxy-3',5'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine  ligand  55  29  .  2021-08-04  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_53T
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 53T  N2    N  N     0  -0.503   6.5892  -1.0029   0.1864
 53T  C8    C  CH3   0  -0.765   3.6347   1.9550   0.7698
 53T  C10   C  CSP   0   0.107   3.0212  -0.5303  -0.6111
 53T  C11   C  CSP   0   0.150   1.9106  -0.7448  -1.0341
 53T  C12   C  CH1   0  -0.509   0.5611  -0.9689  -1.5438
 53T  C13   C  CH3   0  -0.639   0.4831  -0.6908  -3.0531
 53T  C1    C  CR6   0   0.458   5.3680  -1.2312  -0.2836
 53T  C2    C  CH3   0  -0.439  -1.7061   3.9740   1.3067
 53T  C3    C  CR6   0   0.540   6.7885   0.1479   0.8246
 53T  C5    C  CR6   0   0.251   4.6604   0.8878   0.5598
 53T  C6    C  CR6   0  -0.352   4.3246  -0.2857  -0.1150
 53T  C21   C  CR6   0   0.137  -6.5015  -0.1182   0.2041
 53T  C20   C  CR16  0  -0.384  -5.2146   0.3812   0.0192
 53T  C22   C  CR16  0  -0.362  -6.6522  -1.4491   0.5759
 53T  C23   C  CR6   0   0.137  -5.5511  -2.2853   0.7556
 53T  C27   C  CH3   0  -0.726  -5.7445  -3.7211   1.1501
 53T  C24   C  CR16  0  -0.390  -4.2794  -1.7622   0.5598
 53T  C25   C  CR6   0   0.123  -4.0951  -0.4279   0.1927
 53T  C18   C  CR6   0   0.133  -2.7345   0.1160  -0.0034
 53T  C19   C  CR16  0  -0.412  -1.7495  -0.6469  -0.6216
 53T  C17   C  CR16  0  -0.473  -2.4297   1.4063   0.4378
 53T  C16   C  CR6   0   0.427  -1.1504   1.9196   0.2553
 53T  O17   O  O2    0  -0.472  -0.7647   3.1463   0.6535
 53T  C15   C  CR16  0  -0.411  -0.1707   1.1435  -0.3652
 53T  C14   C  CR6   0   0.182  -0.4670  -0.1361  -0.8019
 53T  N4    N  N     0  -0.500   5.8799   1.1100   1.0306
 53T  N7    N  NH2   0  -0.819   8.0163   0.3590   1.3346
 53T  N9    N  NH2   0  -0.824   5.1480  -2.3966  -0.9076
 53T  H8    H  HCH3  0   0.255   2.7761   1.5705   1.3233
 53T  H8A   H  HCH3  0   0.259   4.0562   2.7941   1.3181
 53T  H8B   H  HCH3  0   0.256   3.2542   2.3172  -0.1868
 53T  H12   H  HCH1  0   0.284   0.3140  -2.0239  -1.3852
 53T  H13   H  HCH3  0   0.241   1.1882  -1.3178  -3.5979
 53T  H13A  H  HCH3  0   0.243  -0.5203  -0.9036  -3.4222
 53T  H13B  H  HCH3  0   0.233   0.7129   0.3532  -3.2647
 53T  H2    H  HCH3  0   0.229  -2.0619   3.5295   2.2397
 53T  H2A   H  HCH3  0   0.261  -1.1924   4.9044   1.5357
 53T  H2B   H  HCH3  0   0.228  -2.5675   4.1967   0.6718
 53T  H26   H  HCH3  0   0.248  -7.9358   0.8230  -1.0892
 53T  H26A  H  HCH3  0   0.244  -8.5812   0.3758   0.4830
 53T  H26B  H  HCH3  0   0.244  -7.5214   1.7769   0.3253
 53T  H20   H  HCR6  0   0.243  -5.0873   1.4152  -0.2815
 53T  H22   H  HCR6  0   0.240  -7.6497  -1.8451   0.7355
 53T  H27   H  HCH3  0   0.248  -6.1604  -4.3013   0.3241
 53T  H27A  H  HCH3  0   0.244  -4.8036  -4.1884   1.4383
 53T  H27B  H  HCH3  0   0.245  -6.4376  -3.8139   1.9869
 53T  H24   H  HCR6  0   0.244  -3.4156  -2.3965   0.7221
 53T  H19   H  HCR6  0   0.248  -1.9824  -1.6398  -0.9879
 53T  H17   H  HCR6  0   0.276  -3.1926   1.9796   0.9476
 53T  H15   H  HCR6  0   0.260   0.8247   1.5525  -0.4921
 53T  HN7   H  HNH2  0   0.394   8.7721  -0.2415   1.0554
 53T  HN7A  H  HNH2  0   0.394   8.2537   1.2787   1.6623
 53T  HN9   H  HNH2  0   0.397   5.9314  -2.9845  -1.1351
 53T  HN9A  H  HNH2  0   0.403   4.2922  -2.5506  -1.4127
 53T  C26   C  CH3   0  -0.725  -7.6975   0.7599  -0.0254

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 53T  N2   C1    aromatic  1.328  0.020  1.328
 53T  N2   C3    aromatic  1.331  0.020  1.331
 53T  C8   C5    single    1.495  0.020  1.495
 53T  C10  C11   triple    1.208  0.020  1.208
 53T  C10  C6    single    1.416  0.020  1.416
 53T  C11  C12   single    1.460  0.020  1.460
 53T  C12  C13   single    1.537  0.020  1.537
 53T  C12  C14   single    1.517  0.020  1.517
 53T  C1   C6    aromatic  1.418  0.020  1.418
 53T  C1   N9    single    1.340  0.020  1.340
 53T  C2   O17   single    1.414  0.020  1.414
 53T  C3   N4    aromatic  1.339  0.020  1.339
 53T  C3   N7    single    1.346  0.020  1.346
 53T  C5   C6    aromatic  1.395  0.020  1.395
 53T  C5   N4    aromatic  1.326  0.020  1.326
 53T  C26  C21   single    1.501  0.020  1.501
 53T  C21  C20   aromatic  1.393  0.020  1.393
 53T  C21  C22   aromatic  1.390  0.020  1.390
 53T  C20  C25   aromatic  1.392  0.020  1.392
 53T  C22  C23   aromatic  1.394  0.020  1.394
 53T  C23  C27   single    1.502  0.020  1.502
 53T  C23  C24   aromatic  1.389  0.020  1.389
 53T  C24  C25   aromatic  1.396  0.020  1.396
 53T  C25  C18   single    1.478  0.020  1.478
 53T  C18  C19   aromatic  1.391  0.020  1.391
 53T  C18  C17   aromatic  1.397  0.020  1.397
 53T  C19  C14   aromatic  1.392  0.020  1.392
 53T  C17  C16   aromatic  1.390  0.020  1.390
 53T  C16  O17   single    1.346  0.020  1.346
 53T  C16  C15   aromatic  1.395  0.020  1.395
 53T  C15  C14   aromatic  1.384  0.020  1.384
 53T  C8   H8    single    0.970  0.020  1.090
 53T  C8   H8A   single    0.970  0.020  1.090
 53T  C8   H8B   single    0.970  0.020  1.090
 53T  C12  H12   single    0.970  0.020  1.090
 53T  C13  H13   single    0.970  0.020  1.090
 53T  C13  H13A  single    0.970  0.020  1.090
 53T  C13  H13B  single    0.970  0.020  1.090
 53T  C2   H2    single    0.970  0.020  1.090
 53T  C2   H2A   single    0.970  0.020  1.090
 53T  C2   H2B   single    0.970  0.020  1.090
 53T  C26  H26   single    0.970  0.020  1.090
 53T  C26  H26A  single    0.970  0.020  1.090
 53T  C26  H26B  single    0.970  0.020  1.090
 53T  C20  H20   single    0.930  0.020  1.080
 53T  C22  H22   single    0.930  0.020  1.080
 53T  C27  H27   single    0.970  0.020  1.090
 53T  C27  H27A  single    0.970  0.020  1.090
 53T  C27  H27B  single    0.970  0.020  1.090
 53T  C24  H24   single    0.930  0.020  1.080
 53T  C19  H19   single    0.930  0.020  1.080
 53T  C17  H17   single    0.930  0.020  1.080
 53T  C15  H15   single    0.930  0.020  1.080
 53T  N7   HN7   single    0.890  0.020  1.040
 53T  N7   HN7A  single    0.890  0.020  1.040
 53T  N9   HN9   single    0.890  0.020  1.040
 53T  N9   HN9A  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 53T  C3    N2   C1    117.13  3.000
 53T  H8B   C8   H8A   108.72  3.000
 53T  H8B   C8   H8    106.69  3.000
 53T  H8A   C8   H8    108.73  3.000
 53T  H8B   C8   C5    110.67  3.000
 53T  H8A   C8   C5    110.84  3.000
 53T  H8    C8   C5    111.06  3.000
 53T  C6    C10  C11   180.00  3.000
 53T  C12   C11  C10   180.00  3.000
 53T  H12   C12  C14   107.76  3.000
 53T  H12   C12  C13   107.77  3.000
 53T  C14   C12  C13   110.28  3.000
 53T  H12   C12  C11   107.81  3.000
 53T  C14   C12  C11   111.81  3.000
 53T  C13   C12  C11   111.23  3.000
 53T  H13B  C13  H13A  108.39  3.000
 53T  H13B  C13  H13   108.53  3.000
 53T  H13A  C13  H13   108.30  3.000
 53T  H13B  C13  C12   110.69  3.000
 53T  H13A  C13  C12   110.12  3.000
 53T  H13   C13  C12   110.73  3.000
 53T  N9    C1   C6    120.96  3.000
 53T  N9    C1   N2    117.72  3.000
 53T  C6    C1   N2    121.32  3.000
 53T  H2B   C2   H2A   108.68  3.000
 53T  H2B   C2   H2    108.79  3.000
 53T  H2A   C2   H2    108.79  3.000
 53T  H2B   C2   O17   112.07  3.000
 53T  H2A   C2   O17   106.49  3.000
 53T  H2    C2   O17   111.91  3.000
 53T  N7    C3   N4    116.61  3.000
 53T  N7    C3   N2    116.99  3.000
 53T  N4    C3   N2    126.39  3.000
 53T  N4    C5   C6    122.29  3.000
 53T  N4    C5   C8    117.48  3.000
 53T  C6    C5   C8    120.22  3.000
 53T  C5    C6   C1    116.19  3.000
 53T  C5    C6   C10   122.44  3.000
 53T  C1    C6   C10   121.36  3.000
 53T  C22   C21  C20   118.62  3.000
 53T  C22   C21  C26   120.96  3.000
 53T  C20   C21  C26   120.40  3.000
 53T  H20   C20  C25   119.63  3.000
 53T  H20   C20  C21   119.16  3.000
 53T  C25   C20  C21   121.20  3.000
 53T  H22   C22  C23   119.22  3.000
 53T  H22   C22  C21   119.24  3.000
 53T  C23   C22  C21   121.54  3.000
 53T  C24   C23  C27   121.00  3.000
 53T  C24   C23  C22   118.62  3.000
 53T  C27   C23  C22   120.38  3.000
 53T  H27B  C27  H27A  108.03  3.000
 53T  H27B  C27  H27   107.05  3.000
 53T  H27A  C27  H27   107.53  3.000
 53T  H27B  C27  C23   111.40  3.000
 53T  H27A  C27  C23   111.63  3.000
 53T  H27   C27  C23   111.00  3.000
 53T  H24   C24  C25   119.57  3.000
 53T  H24   C24  C23   119.22  3.000
 53T  C25   C24  C23   121.19  3.000
 53T  C18   C25  C24   120.53  3.000
 53T  C18   C25  C20   120.65  3.000
 53T  C24   C25  C20   118.82  3.000
 53T  C17   C18  C19   119.50  3.000
 53T  C17   C18  C25   119.91  3.000
 53T  C19   C18  C25   120.60  3.000
 53T  H19   C19  C14   119.37  3.000
 53T  H19   C19  C18   120.04  3.000
 53T  C14   C19  C18   120.58  3.000
 53T  H17   C17  C16   121.00  3.000
 53T  H17   C17  C18   118.96  3.000
 53T  C16   C17  C18   120.01  3.000
 53T  C15   C16  O17   115.92  3.000
 53T  C15   C16  C17   119.93  3.000
 53T  O17   C16  C17   124.14  3.000
 53T  C16   O17  C2    118.65  3.000
 53T  H15   C15  C14   120.57  3.000
 53T  H15   C15  C16   119.15  3.000
 53T  C14   C15  C16   120.28  3.000
 53T  C15   C14  C19   119.70  3.000
 53T  C15   C14  C12   121.12  3.000
 53T  C19   C14  C12   119.10  3.000
 53T  C5    N4   C3    116.68  3.000
 53T  HN7A  N7   HN7   117.38  3.000
 53T  HN7A  N7   C3    118.86  3.000
 53T  HN7   N7   C3    119.15  3.000
 53T  HN9A  N9   HN9   117.38  3.000
 53T  HN9A  N9   C1    120.45  3.000
 53T  HN9   N9   C1    119.07  3.000
 53T  H26B  C26  H26A  108.06  3.000
 53T  H26B  C26  H26   107.15  3.000
 53T  H26A  C26  H26   107.34  3.000
 53T  H26B  C26  C21   111.58  3.000
 53T  H26A  C26  C21   111.63  3.000
 53T  H26   C26  C21   110.88  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 53T  CONST_01  C5    C6   C1   N2     0.00   0.0  0
 53T  CONST_02  C5    N4   C3   N2     0.00   0.0  0
 53T  CONST_03  N4    C3   N2   C1     0.00   0.0  0
 53T  CONST_04  N4    C5   C6   C1     0.00   0.0  0
 53T  CONST_05  C6    C1   N2   C3     0.00   0.0  0
 53T  CONST_06  C6    C5   N4   C3     0.00   0.0  0
 53T  CONST_07  C24   C25  C20  C21    0.00   0.0  0
 53T  CONST_08  C18   C25  C20  C21  180.00   0.0  0
 53T  CONST_09  C24   C23  C22  C21    0.00   0.0  0
 53T  CONST_10  C23   C22  C21  C20    0.00   0.0  0
 53T  CONST_11  C23   C24  C25  C20    0.00   0.0  0
 53T  CONST_14  C25   C20  C21  C22    0.00   0.0  0
 53T  CONST_15  C25   C24  C23  C22    0.00   0.0  0
 53T  CONST_16  C18   C25  C24  C23  180.00   0.0  0
 53T  CONST_19  C14   C19  C18  C25  180.00   0.0  0
 53T  CONST_20  C16   C17  C18  C25  180.00   0.0  0
 53T  CONST_21  C15   C14  C19  C18    0.00   0.0  0
 53T  CONST_22  C15   C16  C17  C18    0.00   0.0  0
 53T  CONST_23  C16   C17  C18  C19    0.00   0.0  0
 53T  CONST_24  C16   C15  C14  C19    0.00   0.0  0
 53T  CONST_25  C14   C19  C18  C17    0.00   0.0  0
 53T  CONST_26  C14   C15  C16  C17    0.00   0.0  0
 53T  CONST_27  C10   C6   C1   N2   180.00   0.0  0
 53T  CONST_28  C1    C6   C5   C8   180.00   0.0  0
 53T  CONST_29  C3    N4   C5   C8   180.00   0.0  0
 53T  CONST_30  N4    C5   C6   C10  180.00   0.0  0
 53T  CONST_31  C18   C19  C14  C12  180.00   0.0  0
 53T  CONST_32  C16   C15  C14  C12  180.00   0.0  0
 53T  CONST_33  N7    C3   N2   C1   180.00   0.0  0
 53T  CONST_34  N9    C1   N2   C3   180.00   0.0  0
 53T  CONST_35  N9    C1   C6   C5   180.00   0.0  0
 53T  CONST_36  N7    C3   N4   C5   180.00   0.0  0
 53T  CONST_37  C25   C20  C21  C26  180.00   0.0  0
 53T  CONST_38  C23   C22  C21  C26  180.00   0.0  0
 53T  CONST_39  C27   C23  C22  C21  180.00   0.0  0
 53T  CONST_40  C25   C24  C23  C27  180.00   0.0  0
 53T  CONST_41  O17   C16  C17  C18  180.00   0.0  0
 53T  CONST_42  C14   C15  C16  O17  180.00   0.0  0
 53T  CONST_43  H22   C22  C21  C20  180.00   0.0  0
 53T  CONST_44  H24   C24  C25  C20  180.00   0.0  0
 53T  CONST_45  H20   C20  C21  C22  180.00   0.0  0
 53T  CONST_46  H19   C19  C18  C25    0.00   0.0  0
 53T  CONST_47  H17   C17  C18  C25    0.00   0.0  0
 53T  CONST_48  H15   C15  C14  C19  180.00   0.0  0
 53T  CONST_49  HN9   N9   C1   N2     0.00   0.0  0
 53T  CONST_50  HN9A  N9   C1   N2   180.00   0.0  0
 53T  CONST_51  HN7   N7   C3   N2     0.00   0.0  0
 53T  CONST_52  HN7A  N7   C3   N2   180.00   0.0  0
 53T  Var_01    C17   C16  O17  C2     0.38  30.0  2
 53T  Var_02    H8    C8   C5   C6    58.50  30.0  2
 53T  Var_03    H26   C26  C21  C20   80.80  30.0  2
 53T  Var_04    H27   C27  C23  C22   71.10  30.0  2
 53T  Var_05    H2    C2   O17  C16   61.35  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 53T  chir_01  C12  C11  C13  C14  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 53T  plan-1  N2    0.020
 53T  plan-1  C8    0.020
 53T  plan-1  C10   0.020
 53T  plan-1  C11   0.020
 53T  plan-1  C1    0.020
 53T  plan-1  C3    0.020
 53T  plan-1  C5    0.020
 53T  plan-1  C6    0.020
 53T  plan-1  N4    0.020
 53T  plan-1  N7    0.020
 53T  plan-1  N9    0.020
 53T  plan-2  C21   0.020
 53T  plan-2  C20   0.020
 53T  plan-2  C22   0.020
 53T  plan-2  C23   0.020
 53T  plan-2  C27   0.020
 53T  plan-2  C24   0.020
 53T  plan-2  C25   0.020
 53T  plan-2  C18   0.020
 53T  plan-2  H20   0.020
 53T  plan-2  H22   0.020
 53T  plan-2  H24   0.020
 53T  plan-2  C26   0.020
 53T  plan-3  C12   0.020
 53T  plan-3  C25   0.020
 53T  plan-3  C18   0.020
 53T  plan-3  C19   0.020
 53T  plan-3  C17   0.020
 53T  plan-3  C16   0.020
 53T  plan-3  O17   0.020
 53T  plan-3  C15   0.020
 53T  plan-3  C14   0.020
 53T  plan-3  H19   0.020
 53T  plan-3  H17   0.020
 53T  plan-3  H15   0.020
 53T  plan-4  C3    0.020
 53T  plan-4  N7    0.020
 53T  plan-4  HN7   0.020
 53T  plan-4  HN7A  0.020
 53T  plan-5  C1    0.020
 53T  plan-5  N9    0.020
 53T  plan-5  HN9   0.020
 53T  plan-5  HN9A  0.020

